Vertices Select Highlighting Not Consistent With Rigging
Bones assignements are strictly related to vertex groups:  if you animate a bone named "Head", Blender will search for a vertex group named "Head", as it finds it he will move all the vertices accordingly to every single vertex weight.
So you can select your character, select the armature, Ctrl P for parenting them, then choose the option "with empty group": this will create an empty vertex group named as every bone of the armature: then you can select a group of vertices, go to the vertex tab on the properties menu, select the "Head" vertex group, choose the weight you want with the slider, and click the assign button. 
Note also that in the "N" properties panel of the 3D window, if you select a vertex in edit mode you can read all his weights assignements.